When flying the Zoltan ship, if you get an event with boarders it sometimes justifies bypassing your Super Shields by saying "they must have a Zoltan Shield Bypass installed on their ship!"

Which makes me wonder, is this just a flavour text excuse to justify an otherwise contradictory encounter, or can enemy ships actually have Augments? If the latter, which ships can have which augments?

@Zibbobz That's kinda what my ship would've said just now when fighting the Rebel Flagship, and I had four Zoltan and the Battery active for a total of 33 power in systems!
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Niet the Dark AbsolApr 11 '14 at 18:10

It is a flavor text only. It is worth noting that bypassing the Zoltan shield augment only exists in the AE, but that flavor text is in both standard mode and AE. See z-'s answer for remaining details.